mirror of
https://github.com/MillironX/taxprofiler.git
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578 lines
22 KiB
Text
578 lines
22 KiB
Text
/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Config file for defining DSL2 per module options and publishing paths
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Available keys to override module options:
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ext.args = Additional arguments appended to command in module.
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ext.args2 = Second set of arguments appended to command in module (multi-tool modules).
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ext.args3 = Third set of arguments appended to command in module (multi-tool modules).
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ext.prefix = File name prefix for output files.
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----------------------------------------------------------------------------------------
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*/
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process {
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withName: FASTQC {
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ext.args = '--quiet'
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ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
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publishDir = [
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path: { "${params.outdir}/fastqc/raw" },
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mode: params.publish_dir_mode,
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pattern: '*.{html,zip}'
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]
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}
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withName: FASTQC_PROCESSED {
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ext.args = '--quiet'
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ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
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publishDir = [
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path: { "${params.outdir}/fastqc/processed" },
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mode: params.publish_dir_mode,
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pattern: '*.{html,zip}'
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]
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}
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withName: FALCO {
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ext.prefix = { "${meta.id}_${meta.run_accession}_raw_falco" }
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publishDir = [
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path: { "${params.outdir}/falco/raw" },
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mode: params.publish_dir_mode,
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pattern: '*.{html,txt,zip}'
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]
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}
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withName: FALCO_PROCESSED {
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ext.prefix = { "${meta.id}_${meta.run_accession}_processed_falco" }
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publishDir = [
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path: { "${params.outdir}/falco/processed" },
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mode: params.publish_dir_mode,
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pattern: '*.{html,txt,zip}'
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]
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}
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withName: FASTP_SINGLE {
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ext.args = [
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// trimming options
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params.shortread_qc_skipadaptertrim ? "--disable_adapter_trimming" : "",
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params.shortread_qc_adapterlist ? "" : params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "",
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// filtering options
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"--length_required ${params.shortread_qc_minlength}",
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(params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp') ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
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].join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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[
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path: { "${params.outdir}/fastp" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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],
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[
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path: { "${params.outdir}/fastp" },
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mode: params.publish_dir_mode,
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pattern: '*.{log,html,json}'
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]
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]
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}
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withName: FASTP_PAIRED {
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ext.args = [
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// collapsing options - option to retain singletons
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params.shortread_qc_includeunmerged ? '--include_unmerged' : '',
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// trimming options
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params.shortread_qc_skipadaptertrim ? "--disable_adapter_trimming" : "",
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params.shortread_qc_adapterlist ? "" : params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "",
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params.shortread_qc_adapterlist ? "" : params.shortread_qc_adapter2 ? "--adapter_sequence_r2 ${params.shortread_qc_adapter2}" : "--detect_adapter_for_pe",
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// filtering options
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"--length_required ${params.shortread_qc_minlength}",
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params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp' ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
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].join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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[
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path: { "${params.outdir}/fastp" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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],
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[
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path: { "${params.outdir}/fastp" },
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mode: params.publish_dir_mode,
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pattern: '*.{log,html,json}'
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]
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]
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}
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withName: ADAPTERREMOVAL_SINGLE {
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ext.args = [
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// trimming options
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params.shortread_qc_skipadaptertrim ? "--adapter1 ''" : params.shortread_qc_adapterlist ? "" : params.shortread_qc_adapter1 ? "--adapter1 ${params.shortread_qc_adapter1}" : "",
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// filtering options
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"--minlength ${params.shortread_qc_minlength}"
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].join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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[
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path: { "${params.outdir}/adapterremoval" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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],
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[
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path: { "${params.outdir}/adapterremoval" },
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mode: params.publish_dir_mode,
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pattern: '*.settings'
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]
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]
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}
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withName: ADAPTERREMOVAL_PAIRED {
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ext.args = [
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// collapsing options
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params.shortread_qc_mergepairs ? "--collapse" : "",
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// trimming options
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params.shortread_qc_skipadaptertrim ? "--adapter1 ''" : params.shortread_qc_adapterlist ? "" : params.shortread_qc_adapter1 ? "--adapter1 ${params.shortread_qc_adapter1}" : "", // adding adapter list happens at module input channel level
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params.shortread_qc_skipadaptertrim ? "--adapter2 ''" : params.shortread_qc_adapterlist ? "" : params.shortread_qc_adapter2 ? "--adapter2 ${params.shortread_qc_adapter2}" : "",
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// filtering options
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"--minlength ${params.shortread_qc_minlength}"
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].join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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[
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path: { "${params.outdir}/adapterremoval" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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],
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[
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path: { "${params.outdir}/adapterremoval" },
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mode: params.publish_dir_mode,
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pattern: '*.settings'
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]
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]
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}
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withName: PORECHOP_PORECHOP {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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[
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path: { "${params.outdir}/porechop" },
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mode: params.publish_dir_mode,
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pattern: '*_porechopped.fastq.gz',
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enabled: params.save_preprocessed_reads
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],
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[
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path: { "${params.outdir}/porechop" },
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mode: params.publish_dir_mode,
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pattern: '*.log'
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]
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]
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}
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withName: FILTLONG {
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ext.args = [
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"--min_length ${params.longread_qc_qualityfilter_minlength}",
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"--keep_percent ${params.longread_qc_qualityfilter_keeppercent}",
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"--target_bases ${params.longread_qc_qualityfilter_targetbases}"
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]
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.join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}_filtered" }
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publishDir = [
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[
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path: { "${params.outdir}/filtlong" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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],
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[
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path: { "${params.outdir}/filtlong" },
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mode: params.publish_dir_mode,
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pattern: '*.log'
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]
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]
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}
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withName: BOWTIE2_BUILD {
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publishDir = [
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path: { "${params.outdir}/bowtie2/build" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_index,
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pattern: 'bowtie2'
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]
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}
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// Saving unmapped reads as FQ comes via input channel!
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withName: BOWTIE2_ALIGN {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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[
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path: { "${params.outdir}/bowtie2/align" },
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mode: params.publish_dir_mode,
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pattern: '*.log'
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],
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[
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path: { "${params.outdir}/bowtie2/align" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_bam,
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pattern: '*.bam'
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],
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[
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path: { "${params.outdir}/bowtie2/align" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_unmapped,
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pattern: '*.fastq.gz'
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]
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]
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}
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withName: MINIMAP2_INDEX {
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ext.args = '-x map-ont'
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publishDir = [
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path: { "${params.outdir}/minimap2/index" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_index,
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pattern: '*.mmi'
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]
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}
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withName: MINIMAP2_ALIGN {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/minimap2/align" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_bam,
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pattern: '*.bam'
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]
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}
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withName: SAMTOOLS_VIEW {
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ext.args = '-f 4'
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ext.prefix = { "${meta.id}_${meta.run_accession}.unmapped" }
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}
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withName: SAMTOOLS_BAM2FQ {
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ext.prefix = { "${meta.id}_${meta.run_accession}.unmapped" }
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publishDir = [
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path: { "${params.outdir}/samtools/bam2fq" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_unmapped,
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pattern: '*.fq.gz'
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]
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}
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withName: SAMTOOLS_STATS {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/samtools/stats" },
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mode: params.publish_dir_mode,
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pattern: '*stats'
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]
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}
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withName: BBMAP_BBDUK {
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ext.args = [
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"entropy=${params.shortread_complexityfilter_entropy}",
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"entropywindow=${params.shortread_complexityfilter_bbduk_windowsize}",
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params.shortread_complexityfilter_bbduk_mask ? "entropymask=t" : "entropymask=f"
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].join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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[
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path: { "${params.outdir}/bbduk/" },
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mode: params.publish_dir_mode,
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pattern: '*.{fastq.gz,log}',
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enabled: params.save_complexityfiltered_reads
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],
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[
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path: { "${params.outdir}/bbduk/" },
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mode: params.publish_dir_mode,
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pattern: '*.log'
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]
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]
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}
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withName: PRINSEQPLUSPLUS {
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ext.args = [
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params.shortread_complexityfilter_prinseqplusplus_mode == 'dust' ? "-lc_dust=${params.shortread_complexityfilter_prinseqplusplus_dustscore}" : "-lc_entropy=${params.shortread_complexityfilter_entropy}",
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"-trim_qual_left=0 -trim_qual_left=0 -trim_qual_window=0 -trim_qual_step=0",
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].join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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[
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path: { "${params.outdir}/prinseqplusplus/" },
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mode: params.publish_dir_mode,
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pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz}',
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enabled: params.save_complexityfiltered_reads
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],
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[
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path: { "${params.outdir}/prinseqplusplus/" },
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mode: params.publish_dir_mode,
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pattern: '*.log'
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]
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]
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}
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withName: CAT_FASTQ {
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ext.prefix = { "${meta.id}" }
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publishDir = [
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path: { "${params.outdir}/run_merging/" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_runmerged_reads
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]
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}
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withName: MALT_RUN {
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ext.args = { "${meta.db_params} -m ${params.malt_mode}" }
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// one run with multiple samples, so fix ID to just db name to ensure clean log name
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ext.prefix = { "${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/malt/${meta.db_name}/" },
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mode: params.publish_dir_mode,
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pattern: '*.{rma6,log,sam}'
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]
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}
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withName: 'MEGAN_RMA2INFO_TSV' {
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ext.args = "-c2c Taxonomy"
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ext.prefix = { "${meta.id}" }
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publishDir = [
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path: { "${params.outdir}/malt/${meta.db_name}/" },
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mode: params.publish_dir_mode,
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pattern: '*.{txt.gz,megan}'
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]
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}
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withName: KRAKEN2_KRAKEN2 {
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ext.args = params.kraken2_save_minimizers ? { "${meta.db_params} --report-minimizer-data" } : { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { meta.tool == "bracken" ? "${meta.id}_${meta.db_name}.bracken" : "${meta.id}_${meta.db_name}.kraken2" } : { meta.tool == "bracken" ? "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" : "${meta.id}_${meta.run_accession}_${meta.db_name}.kraken2" }
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publishDir = [
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path: { "${params.outdir}/kraken2/${meta.db_name}/" },
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mode: params.publish_dir_mode,
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pattern: '*.{txt,fastq.gz}'
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]
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}
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withName: BRACKEN_BRACKEN {
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errorStrategy = 'ignore'
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.bracken" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" }
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publishDir = [
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path: { "${params.outdir}/bracken/${meta.db_name}/" },
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mode: params.publish_dir_mode,
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pattern: '*.tsv'
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]
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}
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withName: BRACKEN_COMBINEBRACKENOUTPUTS {
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ext.prefix = { "bracken_${meta.id}_combined_reports" }
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publishDir = [
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path: { "${params.outdir}/bracken/" },
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mode: params.publish_dir_mode,
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pattern: '*.txt'
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]
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}
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withName: KRAKENTOOLS_COMBINEKREPORTS_KRAKEN {
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ext.prefix = { "kraken2_${meta.id}_combined_reports" }
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publishDir = [
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path: { "${params.outdir}/kraken2/" },
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mode: params.publish_dir_mode,
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pattern: '*.txt'
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]
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}
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withName: KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
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ext.args = { "${meta.db_params}" }
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// one run with multiple samples, so fix ID to just db name to ensure clean log name
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ext.prefix = { "${meta.db_name}.krakenuniq" }
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publishDir = [
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path: { "${params.outdir}/krakenuniq/${meta.db_name}/" },
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mode: params.publish_dir_mode,
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pattern: '*.{txt,fastq.gz}'
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]
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}
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withName: KRONA_CLEANUP {
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/krona/" },
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mode: params.publish_dir_mode,
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pattern: '*.{html}'
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]
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}
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withName: KRONA_KTIMPORTTEXT {
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ext.prefix = { "${meta.tool}_${meta.id}" }
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publishDir = [
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path: { "${params.outdir}/krona/" },
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mode: params.publish_dir_mode,
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pattern: '*.{html}'
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]
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}
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withName: 'MEGAN_RMA2INFO_KRONA' {
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ext.args = { "--read2class Taxonomy" }
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ext.prefix = { "${meta.id}_${meta.db_name}" }
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}
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withName: KRONA_KTIMPORTTAXONOMY {
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ext.args = "-i"
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ext.prefix = { "${meta.tool}_${meta.id}" }
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publishDir = [
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path: { "${params.outdir}/krona/" },
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mode: params.publish_dir_mode,
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pattern: '*.{html}'
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]
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}
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withName: METAPHLAN3_METAPHLAN3 {
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.metaphlan3" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.metaphlan3" }
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publishDir = [
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path: { "${params.outdir}/metaphlan3/${meta.db_name}/" },
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mode: params.publish_dir_mode,
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pattern: '*.{biom,txt}'
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]
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}
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withName: METAPHLAN3_MERGEMETAPHLANTABLES {
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ext.prefix = { "metaphlan3_${meta.id}_combined_reports" }
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publishDir = [
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path: { "${params.outdir}/metaphlan3/" },
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mode: params.publish_dir_mode,
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pattern: '*.{txt}'
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]
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}
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withName: CENTRIFUGE_CENTRIFUGE {
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publishDir = [
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path: { "${params.outdir}/centrifuge/${meta.db_name}/" },
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mode: params.publish_dir_mode,
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pattern: '*.{txt,sam,gz}'
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]
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
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}
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withName: CENTRIFUGE_KREPORT {
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errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'}
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
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publishDir = [
|
|
path: { "${params.outdir}/centrifuge/${meta.db_name}/" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.{txt}'
|
|
]
|
|
}
|
|
|
|
withName: KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE {
|
|
errorStrategy = { task.exitStatus in [255,1] ? 'ignore' : 'retry' }
|
|
ext.prefix = { "centrifuge_${meta.id}_combined_reports" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/centrifuge/" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.{txt}'
|
|
]
|
|
}
|
|
|
|
withName: KAIJU_KAIJU {
|
|
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.kaiju" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.kaiju" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/kaiju/${meta.db_name}/" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.tsv'
|
|
]
|
|
ext.args = { "${meta.db_params}" }
|
|
}
|
|
|
|
withName: '.*PROFILING:KAIJU_KAIJU2TABLE' {
|
|
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.kaijutable" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.kaijutable" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/kaiju/${meta.db_name}/" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.{txt}'
|
|
]
|
|
}
|
|
|
|
withName: '.*STANDARDISATION_PROFILES:KAIJU_KAIJU2TABLE' {
|
|
ext.prefix = { "kaiju_${meta.id}_combined_reports" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/kaiju/" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.{txt}'
|
|
]
|
|
}
|
|
|
|
withName: KAIJU_KAIJU2KRONA {
|
|
ext.args = '-v -u'
|
|
}
|
|
|
|
withName: DIAMOND_BLASTX {
|
|
ext.args = { "${meta.db_params}" }
|
|
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.diamond" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.diamond" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/diamond/${meta.db_name}/" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.{blast,xml,txt,daa,sam,tsv,paf,log}'
|
|
]
|
|
}
|
|
|
|
withName: MOTUS_PROFILE {
|
|
ext.args = {
|
|
[
|
|
params.motus_remove_ncbi_ids ? "" : "-p",
|
|
params.motus_use_relative_abundance ? "" : "-c",
|
|
params.motus_save_mgc_read_counts ? "-M ${task.ext.prefix}.mgc" : ""
|
|
].join(',').replaceAll(','," ")
|
|
}
|
|
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/motus/${meta.db_name}/" },
|
|
mode: params.publish_dir_mode
|
|
]
|
|
}
|
|
|
|
withName: MOTUS_MERGE {
|
|
ext.args = { params.standardisation_motus_generatebiom ? "-B" : "" }
|
|
ext.prefix = { "motus_${meta.id}_combined_reports" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/motus/" },
|
|
mode: params.publish_dir_mode
|
|
]
|
|
}
|
|
|
|
withName: TAXPASTA_MERGE {
|
|
ext.args = {
|
|
[
|
|
"-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}",
|
|
params.taxpasta_taxonomy_dir ? "--taxonomy ${params.taxpasta_taxonomy_dir}" : "",
|
|
params.taxpasta_add_name ? "--add-name" : "",
|
|
params.taxpasta_add_rank ? "--add-rank" : "",
|
|
params.taxpasta_add_lineage ? "--add-lineage" : "",
|
|
params.taxpasta_add_idlineage ? "--add-id-lineage" : ""
|
|
].join(' ').trim()
|
|
}
|
|
publishDir = [
|
|
path: { "${params.outdir}/taxpasta/" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.{tsv,csv,arrow,parquet,biom}'
|
|
]
|
|
}
|
|
|
|
withName: CUSTOM_DUMPSOFTWAREVERSIONS {
|
|
publishDir = [
|
|
path: { "${params.outdir}/pipeline_info" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*_versions.yml'
|
|
]
|
|
}
|
|
|
|
withName: MULTIQC {
|
|
publishDir = [
|
|
path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
|
|
]
|
|
}
|
|
}
|